The problems I'm referring to relate to one specific device, widely sold I understand. If you're getting your problem with different devices, then it's something else.
Could I suppose be something to do with the MU50, but I don't know what.
Does not sound like it's anything to do with MIDI.
Sounds to me more like there's a component in the MU that, once it warms up, is starting to fail. Might even be a solder joint somewhere, they too can be affected by temperature. Can you open the MU up, i.e. take the cover off, and cool it with a fan (not too drastically), and see if it works OK for longer? How long has the problem been happening for, was it worse when it was warmer than cooler (or vice-versa dep on where in the world you are.
You tend to think that these sort of boxes will last for ever, but that's not the case. They can suffer from 'old-age'. Can of course be fixed by those who know about this sort of thing, but may not be easy to do for specialised pieces of gear. Yamaha do at least have a network of repair agents (more re keyboards etc) but they should be able to take care of something like a MU device.
An extra thought. When the MU starts to misbehave, if you try to play the demo songs then, what do they do? The answer may help narrow down which part of the unit has the problem.